VX Hydrolysis by Human Serum Paraoxonase 1: A Comparison of Experimental and Computational Results

Abstract

Human Serum paraoxonase 1 (HuPON1) is an enzyme that has been shown to hydrolyze a variety of chemicals including the nerve agent VX. While wildtype HuPON1 does not exhibit sufficient activity against VX to be used as an in vivo countermeasure, it has been suggested that increasing HuPON1's organophosphorous hydrolase activity by one or two orders of magnitude would make the enzyme suitable for this purpose. The binding interaction between HuPON1 and VX has recently been modeled, but the mechanism for VX hydrolysis is still unknown. In this study, we created a transition state model for VX hydrolysis (VXts) in water using quantum mechanical/molecular mechanical simulations, and docked the transition state model to 22 experimentally characterized HuPON1 variants using AutoDock Vina. The HuPON1-VXts complexes were grouped by reaction mechanism using a novel clustering procedure. The average Vina interaction energies for different clusters were compared to the experimentally determined activities of HuPON1 variants to determine which computational procedures best predict how well HuPON1 variants will hydrolyze VX. The analysis showed that only conformations which have the attacking hydroxyl group of VXts coordinated by the sidechain oxygen of D269 have a significant correlation with experimental results. The results from this study can be used for further characterization of how HuPON1 hydrolyzes VX and design of HuPON1 variants with increased activity against VX.

Molecular Dynamics Approach in the Comparison of Wild-Type and Mutant Paraoxonase-1 Apoenzyme Form

“…They in fact decreased clearly in the case of PON1mut since mutations appear to suppress the movement of the two loops responsible for catalytic activation. This result provides more evidence on the involvement of L1 and L2 loops in the overall flexibility of the PON1mut and brings insights to the loops disorders additional to the ones described in the studies by Peterson et al 22 and Sanan et al 23 In line with these analyses, useful information about the PON1mut conformations have been gained from examining the trajectories. The PON1mut adopts a closed conformation all over the time of dynamics simulation following a short open-closed period at the beginning of the simulation.…”

Catalytic Versatility and Backups in Enzyme Active Sites: The Case of Serum Paraoxonase 1

“…However, these were all based on the pH 4.5 structure in which the loop is disordered. [24][25][26][27] The structure of the 2HQ complex reveals that the loop adopts a different conformation from those predicted.…”

Catalytic mechanisms for phosphotriesterases

“…The active site residues L69, H115, and H184 from the large side pocket, F222 and F292 from the central pocket and residues, H285 and V346 from the small pocket appear most important for phosphotriesterase activity [23,85,91]. Directed evolution of the active site of PON1 has yielded improved activity against the nerve agents GD, GF and VX [85,86,88]. With GF, the activity against the most toxic enantiomer was improved more than 2-orders of magnitude to ~10 5 M −1 s −1 [86].…”